4RXT

Crystal structure of carbohydrate transporter solute binding protein Arad_9553 from Agrobacterium Radiobacter, Target EFI-511541, in complex with D-arabinose

• PDB DOI: https://doi.org/10.2210/pdb4RXT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rhizobium rhizogenes K84
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-11 Released: 2014-12-24 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.205 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.25 kDa 
• Atom Count: 2,515 
• Modelled Residue Count: 295 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter	A	299	Rhizobium rhizogenes K84	Mutation(s): 0  Gene Names: Arad_9553
UniProt
Find proteins for B9JKX8 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9JKX8  Go to UniProtKB:  B9JKX8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARA	B [auth A]	alpha-L-arabinopyranose C5 H10 O5 SRBFZHDQGSBBOR-QMKXCQHVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.205 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.873	α = 90
b = 36.244	β = 110.01
c = 62.1	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Structure summary